The best preamble is the preamble, that does contain only these packages and definitions you are using. BTW: You should read l2tabu to avoid obsolete packages like t1enc (use \usepackage[T1]{fontenc} instead). And it would be better to use packages like geometry or typearea to setup text area and margins. At least better use \setlength to set lengths instead of using low level TeX.
– SchweinebackeNov 8 '11 at 16:00

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Paper and page dimensions are better set up by the geometry package. The t1enc package is obsolete and should be replaced by the fontenc package.
– Thorsten DonigNov 8 '11 at 16:02

@Seamus Couldn't agree with you more on this one, although there is value not to add too many packages until you have written 100 or so pages, as by then you know what you need.
– Yiannis LazaridesNov 8 '11 at 16:52

Just to add to the comments of the other posters. Just add packages as you need. A thesis preamble is bound to expand fast. Divide it into sections such as General, Typography, Mathematics, Commands etc. As the preamble grows some of these you will pass to a package say moremath.sty.

Keep the style simple, no fancy fonts. Under typography you can include microtype and stmarysd. Under mathematics you have included the basis and I will second Mico's suggestion of mathtools. Under commands put all your specials. For example under theorems you should include all your formatting decisions as well. As a bonus, here is some styling for theorems.

In addition to the math-related packages you're already loading, you may want to take a look at the mathtools package. It's a superset of the amsmath package. If you load mathtools, there's no need to load amsmath by hand.

You seem to be comfortable with Computer Modern/Latin Modern fonts. If this assumption is correct, you may want to load the lmodern package.

Moreover, instead of loading the deprecated t1enc package, you should issue the instruction \usepackage[T1]{fontenc}.

You should take a look at the geometry package and its margin-setting commands, to let you simplify the setup of the page layout. (As of now, the collection of commands looks like it was thrown together haphazardly.)

What I'd really want to question about your preamble is the use of \pagestyle{empty}. Does your school require this? If not, please do your readers a favor and delete this command, so that LaTeX can print page numbers.